A second genesis? No proof yet, but …

TONY AUTH / The Philadelphia Inquirer (tauth@phillynews.com)

It looked - for a moment - like one of science's deepest questions was cracking open last December. That's when a NASA-funded team announced that it had found a completely new kind of life in California's arsenic-rich Mono Lake.

At a news conference, the researchers said they had discovered an arsenic-based organism - its very DNA infused with the toxic metal. In touting their own findings, they left many viewers with the impression that this bug had sprung from nonliving matter independent of all known life.

The finding of a second origin of life, if real, would have dramatically broadened the view of how life got here and whether it might arise spontaneously elsewhere in the universe.

Unfortunately, to biologists, this "new" form of life looks suspiciously like the old one. And so there remains a gap in our understanding that has prompted several readers to question how scientists can be so confident that evolution explains everything.

"Since life originating from nonlife can't be proven, if it was a one-time phenomenon, what is the scientific basis for ruling out intelligent design? Is it a matter of personal opinion or true objectivity?" wrote Damien Manno of Sicklerville, Camden County

It's a good question, and the short answer is that scientists may soon begin to grasp how life could originate from nonlife. "It's going to be hard to prove that on this day 4.05 billion years ago, this molecule begat that molecule," said biochemist Gerald Joyce of the Scripps Research Institute in La Jolla. "But as far as proving nonlife can give rise to life - absolutely that's going to be proven, because it's going to be done."

In which case, putting God into that gap in our knowledge would leave him on the outside when it slams shut.

The biologists concede, however, that understanding the origin of life would be a lot easier if we lived on a planet where it had happened in more than one way, giving us multiple trees of life. "It's weird there's only one form of life," said Joyce. DNA evidence shows that humans, cats, algae, mushrooms, and every other living thing share enough genetic code to prove we're children of a common ancestor.

Even the much-ballyhooed arsenic bacteria is rooted in the same tree of life, according to its DNA.

Chemist Steven Benner of the Foundation for Applied Molecular Evolution (FFAME) in Gainesville, Fla., said that in trying to search for life on Mars and beyond, scientists assume alien life might not use exactly the same chemical components as Earth life. To avoid missing exotic forms of life elsewhere, they want to draw a broad enough definition.

NASA defines life as a self-sustaining chemical system capable of Darwinian evolution. Not everyone agrees with that, Benner said, but he thinks it works.

One reason we don't see more recent origins of life is that the Earth's atmosphere has changed too much from the time life started, said Joyce. It's now full of oxygen, which wasn't present on the early Earth and would have been toxic to the first organisms.

Some biologists say there might have been multiple origins of life early on, but the other versions of life either went extinct or retreated to remote niches. A few are busy searching for a "shadow biosphere" deep underground, underwater, below Antarctica's lakes, or in another place hostile to known life.

Others, including Joyce, are trying to produce an origin of life in the lab - seeking a mix of chemicals that will assemble itself into something more-or-less alive.

This quest goes all the way back to 1953, when a 23-year-old graduate student named Stanley Miller set out to re-create creation with a simple apparatus composed of two connected glass chambers. One he filled with water, the other with his approximation of the early atmosphere - hydrogen, ammonia, and methane.

He shot an electric current through the apparatus, imitating lightning. Although nothing came to life, chemical reactions in the chamber produced some of the building blocks of living things - amino acids.

Scientists have kept trying. They now see the origin of life as a gradual process - with Darwinian evolution first acting on complex chemicals. Chemicals, in essence, evolved into life. Exactly when matter made the leap from inanimate to animate may be impossible to pin down.

At some point, Joyce said, molecules acquired memory - the ability to store and pass on information. That's what DNA does with its four-letter chemical code. Small copying errors spawn variety, and with that, Darwinian evolution can start.

"The chemical logic is already laid out for how chemistry turns into biology," he said.

The prevailing view is that our DNA-based life was preceded by something called the RNA world - a population of organisms, or proto-organisms, that stored information using this single-stranded relative of DNA's double-stranded helix.

While DNA can't reproduce itself without outside catalysts, scientists have found a type of RNA, called a ribozyme, that can act as its own catalyst to copy itself.

But RNA is thought to be too complex to have sprung up, fully formed, from the primordial soup, so some biologists are trying to construct simpler versions. Christopher Switzer of the University of California Riverside has created FNA - something like DNA but with different "backbone" structures holding it together. He and others have created a whole variety of these - dubbed TNA, PNA, GNA, and so on.

Switzer and Benner, of FFAME, have both made new versions of DNA with extra code-carrying chemical units, called bases, rather than the four that our life uses. Switzer has made one that uses six coding characters. Benner has made one with twelve.

This type of work was even incorporated in the movie E.T., Benner noted; the doctor examining the alien finds six coding elements in his DNA, rather than four.

None of these new versions of DNA has worked in an actual life-form, but that could change.

Last year, J. Craig Venter of the J. Craig Venter Institute announced he'd taken a step in that direction. He and colleagues used laboratory chemicals to synthesize a replica of bacterial DNA, inserted it into related bacteria with its own DNA removed, and watched it come to life.

Then, last December, scientists claimed they had discovered an arsenic-based life-form. The researchers said they had substituted arsenic for phosphorus in the DNA and other critical parts of the cell, the way silicon sometimes substitutes for carbon in creatures from science fiction.

The paper describing the bacteria was supposed to be published in the journal Science last year, but amid much criticism, the journal held off until last week, when the paper appeared with eight rebuttals.

In an interview last week, lead author Felisa Wolfe-Simon admitted that her team doesn't know how much arsenic is actually substituting for phosphorus, and that it may be a small amount.

Biologists who have read the paper say her team never conducted the tests needed to show any arsenic is truly incorporated in the RNA or DNA. The bacteria were still exposed to some phosphorus as a contaminant - enough to supply the production of normal DNA.

Beyond that, some say other strains of bacteria are known to survive in much more concentrated solutions of arsenic, and they find ways to do this without becoming "arsenic based."

So any hope that the arsenic bacteria represent a second genesis is dead. But the search goes on.

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